The present invention provides a supported metal catalyst with synergistic sites, a preparation method therefor and an application thereof. The preparation method of this catalyst is to utilize the unsaturated cubane-like structure, M cation with catalytic activity is introduced into the cluster core unit. By using the vertex vacancy as the capturing center, and adjusting the impregnation temperature to maximize the loading of the cluster precursor, as well as depending on the electrostatic adsorption of the support and the confinement of the cluster structural unit, the number of S vacancies and the distance between S vacancies and Miso sites are effectively controlled through liquid phase reduction and atmosphere treatment at room temperature to obtain supported X3MSx/Al2O3 catalyst with Miso-Vs synergistic sites. The method of the present invention achieves the joint enhancement of the activity, product selectivity, and stability of unsaturated carbon oxygen bond selective hydrogenation, carbon chlorine bond selective hydrogenation dechlorination, and carbon hydrogen bond dehydrogenation reactions. This catalyst is mainly used in various catalytic reaction processes in the fields of petrochemical, fine chemical, environmental chemical, and other fields. It has outstanding catalytic performance, excellent activity, selectivity, and good recyclability, and is easy to recover and reuse.